It means that the fact the payment is made does not mean that it indicates any admission of liability and should not be taken as any signal of future intentions. This often applies to the holiday business, for example you go on holiday and you are not entirely happy and you complain to the holiday firm. Now the things that made you unhappy may not have been within their control but often they will make a small payment as compensation. There is nothing forcing them to do so and in doing so they are not admitting any wrong doing, ie it is simply an "ex-gratia payment without prejudice"